fix(json): audit and standardize JSON output across commands (bd-au0.7)

Audit findings:
- All commands properly respect --json flag for success output
- Added outputJSONError() helper for consistent JSON error output
- Removed redundant local --json flag from stale.go (inherited from rootCmd)
- Fixed stale_test.go to check InheritedFlags() instead of local Flags()

JSON output patterns verified across:
- Query commands: ready, blocked, stale, count, stats, status
- Dep commands: dep add/remove/tree/cycles
- Label commands: label add/remove/list/list-all
- Comment commands: comments add/list
- Epic commands: epic status/close-eligible

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

cmd/bd/autoflush.go

@@ -33,6 +33,24 @@ func outputJSON(v interface{}) {
 	}
 }
 
+// outputJSONError outputs an error as JSON to stderr and exits with code 1.
+// Use this when jsonOutput is true and an error occurs, to ensure consistent
+// machine-readable error output. The error is formatted as:
+//
+//	{"error": "error message", "code": "error_code"}
+//
+// The code parameter is optional (pass "" to omit).
+func outputJSONError(err error, code string) {
+	errObj := map[string]string{"error": err.Error()}
+	if code != "" {
+		errObj["code"] = code
+	}
+	encoder := json.NewEncoder(os.Stderr)
+	encoder.SetIndent("", "  ")
+	_ = encoder.Encode(errObj)
+	os.Exit(1)
+}
+
 // findJSONLPath finds the JSONL file path for the current database
 // findJSONLPath discovers the JSONL file path for the current database and ensures
 // the parent directory exists. Uses beads.FindJSONLPath() for discovery (checking